[R] MSM package and qmatrix

[Peter Adamson]

Hi Ross,

For an eleven state model you could define transitions as follows:

transitions_allowed <- matrix(c(
                          0,1,1,1,1,1,1,1,1,1,1,
                          1,0,1,1,1,1,1,1,1,1,1,
                          1,1,0,1,1,1,1,1,1,1,1,
                          1,1,1,0,1,1,1,1,1,1,1,
                          1,1,1,1,0,1,1,1,1,1,1,
                          1,1,1,1,1,0,1,1,1,1,1,
                          1,1,1,1,1,1,0,1,1,1,1,
                          1,1,1,1,1,1,1,0,1,1,1,
                          1,1,1,1,1,1,1,1,0,1,1,
                          1,1,1,1,1,1,1,1,1,0,1,
                          1,1,1,1,1,1,1,1,1,1,0
                          ), nrow=11, ncol=11,
                          byrow=TRUE,
                          dimnames=list(from=1:11,to=1:11))


In your case - I think you may be getting the error message as you have 23
200 201 203 999 as states and not 1 2 3 4 5 6 7 8 9 10.  Try recoding 23 200
201 203 999 to 6 7 8 9 10?

HTH, Peter


Ross Culloch wrote:
> 
> Hi R-helpers,
> 
> I am having a problem understanding how to construct the qmatrix, i have
> read the help menu for msm but I am still a bit lost. Below is an example
> of one of my transition matrices:
> 
> statetable.msm(BEH, ID, data = A1)
> 
>      to
> from   1  2  3  4  5 23 200 201 203 999
>   1   86 11  2 20  1  9   3  11   1  22
>   2   18  4  4  4  0  1   1   1   0   1
>   3    5  2  0  5  0  0   2   0   0   3
>   4   17  5  5 13  0  4   3   3   0   7
>   5    1  0  1  1  0  0   0   0   0   0
>   23   7  3  0  4  0  3   1   3   0   3
>   200  5  0  2  3  1  2   1   3   0   3
>   201  5  5  3  2  1  0   2   6   1   5
>   203  3  0  0  0  0  0   0   0   0   0
>   999 18  4  0  5  0  5   7   3   1   0
> 
> 
> Instantaneous transition IS allowed from state r to state s. But what i
> don't understand is what is the logical way to create the initial
> transition matrix - i've tried to just give even numbers to all transition
> possibilities e.g. every transition given 0.1 or 1, but i get the
> following error message:
> 
>  Error in msm.check.state(nrow(qmatrix), state, cens$censor) : 
>   State vector contains elements not in 1, 2, ... , 10
> 
> Does anyone have any suggestions, i can only assume that this is a simple
> problem that i have overlooked because nobody else seems to have asked it!
> 
> Any suggestions on how to construct a qmatrix would be much appreciated,
> 
> Berst wishes,
> 
> Ross
> 

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